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342 results for “extracellular matrix”
Data description: Deprivation of loading during early healing of rat Achilles tendons affects extracellular matrix composition and structure, and reduces cell density and cell alignment
<p><a name="_Hlk158643946"></a><strong>Data description: Deprivation of loading during early healing of rat Achilles tendons affects extracellular matrix composition and structure, and reduces cell density and cell alignment</strong></p> <p><em>Malin Hammerman, Maria Pierantoni, Hanna Isaksson<sup> *</sup>, Pernilla Eliasson <sup>*</sup></em></p> <p><em><sup>* </sup></em><em>joint<sup> </sup>last authors</em></p> <p>This dataset contains microscope images obtained from sections of healing and intact rat Achilles tendons undergoing different in vivo loading protocols and different time points post-transection. The data presented are the full resolution microscope images available in lower resolution in the accompanying manuscript’s Supplementary Figures 4-6.</p> <p>Each zipped folders contain images (tif-files) from all time-points for each respective staining and loading group. </p> <ul> <li>Col1: Sections stained with Collagen 1 antibodies</li> <li>Col3: Sections stained with Collagen 3 antibodies</li> <li>Elastin: Sections stained with Elastin antibodies</li> <li>Full_loading: Free cage activity</li> <li>Reduced_loading: Paralysis of the calf muscle with Botox</li> <li>Minimal_loading: Botox combined with joint fixation using a steel-orthosis</li> <li>Intact_reference: Contralateral uninjured Achilles tendons, used as reference</li> </ul> <p>More description of the datasets inside the zipped files are available below and in the file 'Data Description.pdf'</p> <p> </p> <p><strong>Brief re-cap of methods</strong></p> <p>Histological analysis was performed on healing Achilles tendons from Female Sprague-Dawley rats, specific-pathogen free (11-12 weeks, weight 299 ± 15 g), that had undergone full transection [13] of the right Achilles tendon, and been exposed to different levels of loading. Altered loading was imposed through two mechanisms. Reduced loading involved intramuscular Botox injections in the right calf muscles to induce plantar flexor muscle paralysis [24]. Additionally, the rats in the minimal loading group received a steel-orthosis around their right hindlimb directly after surgery [24].</p> <p>Snap frozen tendons in OCT were sectioned longitudinally (7 μm thickness) and stained with immunofluorescent staining for collagen 1, collagen 3, or elastin. Sections were counterstained with DAPI followed by mounting. The tissue sections were imaged under a microscope (DMi8, Leica Microsystems, Wetzlar, Germany, with a Hamamatsu Orca LT Flash sCMOS camera) where fluorescence was detected at 550 nm (secondary antibody Alexa Fluor 594), 470 nm (secondary antibody Alexa Fluor 488) and 385 nm (DAPI), and exposure time was held constant for each color channel regarding magnification and staining.</p> <p>Mapping images of the entire tendon were obtained for one section per group (n=1 per healing time, loading group and ECM matrix protein). All images were adjusted to the negative control, where the primary antibody was omitted, to correct for unspecific antibody detection.</p> <p><strong>Microscope images and description of file-names </strong></p> <p>All data is presented in the form of .tif files. Please refer to the scale bars in the images. All image-files are named using the following abbreviations, as described below. As an example, the file name “Tendon_col1_FL_1W_col1.tif” refers to a tendon section stained for collagen 1 from a rat exposed to full loading for a period of 1 week after tendon transection, where only the channel for collagen 1 is shown, whereas “Tendon_col1_FL_1W_merged.tif” includes the channels for both staining for collagen 1 and DAPI of the same section.</p> <p>Col1: Sections stained with Collagen 1 antibodies<br>Col3: Sections stained with Collagen 3 antibodies<br>Elastin: Sections stained with Elastin antibodies<br>dapi: Sections stained with 4',6-Diamidino-2-Phenylindole Dihydrochloride.<br>FL: Full loading (free cage activity),<br>RL: Reduced loading (paralysis of the calf muscle with Botox),<br>ML: Minimal loading (Botox combined with joint fixation using a steel-orthosis)<br>IT: Intact contralateral Achilles tendons, used as reference.</p> <p>1W: Healing time point 1 week after transection<br>2W: Healing time point 2 weeks after transection<br>3W: Healing time point 3 weeks after transection<br>20W: Healing time point 20 weeks after transection</p> <p><strong>Settings for brightness and contrast</strong></p> <p><em>Collagen 1</em><br>1w FL 2000-12 000, UL 4000-10 000, ML 4000-12 000<br>2w FL 2500-10 000, UL 4000-10 000, ML 5000-12 000<br>3w FL 2000-12 000, UL 3500-13 000, ML 3500-14 000<br>12w FL 3000-12 000<br>20w FL 3000-11 000<br>IT 2000-8 000</p> <p>Collagen 3<br>1w FL 3000-12 000, UL 4000-10 000, ML 4000-13 000<br>2w FL 2000 - 7 000, UL 2500-12 000, ML 2000-12 000<br>3w FL 2000-12 000, UL 3500-13 000, ML 3500-14 000<br>12w FL 3000-12 000<br>20w FL 2000-12 000<br>IT 3000-12 000</p> <p>Elastin<br>1w FL 4000-10 000, UL 5000 - 8000, ML 3500-12 000<br>2w FL 3000-12 000, UL 3000-12 000, ML 3000-12 000<br>3w FL 2500-12 000, UL 2000-12 000, ML 2500-12 000,<br>12w FL 3500-12 000<br>20w FL 3500-12 000<br>IT 2000-12 000</p>
Small extracellular vesicles from malignant ascites of patients with advanced ovarian cancer provide insights into the dynamics of the extracellular matrix
<p>Representative Atomic Force Microscope images collected in liquid on Extracellular Vesicles from Ascite and Cell cultures. Data were collected by Broker Multimode VIII. Images like these were used in the paper to measure the contact angle and size distribution.</p>
Figure. The phylogenetic tree showing the relationship among Brevibacillus parabrevis strains SA2.2 and TJ2.3, Bacillus licheniformis MG4.2, and their phylogenetically closest type strains. The GenBank accession numbers of the type strains and studied strains are shown following species names. Distance matrix was calculated by Kimura's 2-parameter model. The scale bar indicates 0.02 substitutions per nucleotide position. Alicyclobacillus pohliae AJ564766 served as an out-group. in Distribution of extracellular enzyme-producing bacteria in the digestive tracts of 4 brackish water fish species
Figure. The phylogenetic tree showing the relationship among Brevibacillus parabrevis strains SA2.2 and TJ2.3, Bacillus licheniformis MG4.2, and their phylogenetically closest type strains. The GenBank accession numbers of the type strains and studied strains are shown following species names. Distance matrix was calculated by Kimura's 2-parameter model. The scale bar indicates 0.02 substitutions per nucleotide position. Alicyclobacillus pohliae AJ564766 served as an out-group.
A mathematical model to predict network growth in physarum polycephalum as a function of extracellular matrix viscosity, measured by a novel viscometer
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Effect of long-term physical disability and aging on extracellular matrix biogenesis in human skeletal muscle
<p>Supplemental Table for a study <strong>Effect of long-term physical disability and aging on extracellular matrix biogenesis in human skeletal muscle</strong></p>
The entanglement of extracellular matrix molecules and immune checkpoint inhibitors in cancer: a systematic review of the literature
<p><strong>The datasets include the results obtained upon a literature search on different databases: Web of science, Scopus and Pubmed.</strong></p> <p>The combination of mesh terms searched in the databases were “extracellular matrix molecules” or “extracellular matrix remodeling” and “immune checkpoint inhibitors” or “immunotherapy”.</p>
LifeNet: Extracellular Matrix Graft in Rotator Cuff Repair
ClinicalTrials.gov study NCT03551509. IPD Sharing: NO. Countries: 1. Publications: 14.
A Post Market Study on the Use of Cormatrix® Cangaroo ECM® (Extracellular Matrix) Envelope
ClinicalTrials.gov study NCT02530970. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Effect of Nintedanib on Biomarkers of Extracellular Matrix Turnover in Patients With Idiopathic Pulmonary Fibrosis and Limited Forced Vital Capacity Impairment
ClinicalTrials.gov study NCT02788474. IPD Sharing: YES. Countries: 13. Publications: 4.
Obtain Additional Information on Use of CorMatrix ECM (Extracellular Matrix)
ClinicalTrials.gov study NCT02073331. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A temporary cholesterol-rich diet and bacterial extracellular matrix factors favor Salmonella spp. biofilm formation in the cecum
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The Effect of Extracellular Matrix Stiffness on Inducing Adipogenic Differentiation of ADSCs
<p>Extracellular matrix (ECM) is a critical biophysical factor in adipose-derived stem cells differentiation. However, the specific regulatory mechanisms and signaling pathways of Yes-associated protein (YAP) are unknown, though it plays a critically important role in ECM-induced differentiation. Here, we embedded ADSCs in collagen hydrogels with varying stiffness, elastic moduli, to be exact, of 61Pa, 217Pa, and 321Pa. The expression of adipogenic-specific genes was highly correlated with stiffness of ECM<span>,</span> in addition, our study has found that the levels of YAP phosphorylation were significantly altered on the 9th day after stimulation with ECM stiffness. Staining of lipid droplets with BODIPY indicates that accumulation of lipid droplets depended on hydrogel stiffness; the most pronounced accumulation was registered in 321Pa hydrogels. By inhibiting the YAP signaling pathway, we found that lipid droplet accumulation increased; thus, inhibition of YAP signaling increased YAP phosphorylation in the cytoplasm, thereby promoting accumulation of lipid droplets. In conclusion, YAP played a crucial role in regulating ECM stiffness-induced adipogenic differentiation. Adipose stem cells are differentiated in a microenvironment that offers new insights into their differentiation process. </p>
A simple framework for agent-based modeling with extracellular matrix: Simulation results
<h1>Data for "A simple framework for agent-based modeling with extracellular matrix"</h1> <p> </p> <div>Metzcar, J., Duggan, Ben S., Fischer, B., Murphy, M., Heiland, R., Macklin, P. A simple framework for agent-based modeling with extracellular matrix. bioRxiv. doi: 10.1101/2022.11.21.514608</div> <div> </div> <div><a href="https://www.biorxiv.org/content/10.1101/2022.11.21.514608">Link to preprint</a></div> <div> <p>This repository contains the data for each subfigure (and video) in the preprint cited and linked abvoe, as well as the original figures and videos themselves. We have tried to include original model file (<code>PhysiCell_settings.xml</code> or other <code>*.xml</code> file) used to generate each results with each file set as well as the code (see python scripts) to make images and videos that appear in the pre-print - both within the files and base modules and examples in a separate folder.</p> <p>The data can be regenerated using release 2.0, <a href="https://github.com/PhysiCell-Models/collective-invasion/releases/tag/v2.1">2.1</a>, and <a href="https://github.com/PhysiCell-Models/collective-invasion/releases/tag/v2.2.1">2.2.1</a>. Release 2.1 is recommended for reproducing more exactly the results for the fibrosis, invasive carcinoma, and series of leader-follower results as the results archived here were produced using a set of two random number generators (one from PhysiCell and one from BioFVM). 2.2.1, used to produce the invasive cellular front results, consolidates the use of random number generators to just one (the PhysiCell one). As such, in 2.2.1, the random number generator seed may need changed to produce stochastic replicates, even when multithreading.</p> </div> <p> </p> <div>The following file sets are in this download:</div> <ul> <li>Fig2_SM_3_simple_tests.zip <ul> <li>Has results for Figure 2 and SM Figure 3</li> </ul> </li> <li>Fig3_fibrosis.zip <ul> <li>Results from fibrosis simulation (originally Figure 3, now Figure 4)</li> </ul> </li> <li>Fig4_invasive_carcinoma.zip <ul> <li>Results from invasive carcinoma simulation (originally Figure 4, now Figure 5)</li> </ul> </li> <li>Fig5_collective_migration_initial_tests.zip <ul> <li>Results from initial leader follower model development (originally Figure 5, now Figure 6)</li> </ul> </li> <li>Fig6_instant_remodeling.zip <ul> <li>Results from instant remodeling leader follower model scenariods (originally Figure 6, now Figure 7)</li> </ul> </li> <li>Fig7b_leader_follower.zip <ul> <li>Results from leader-follower collective migration scenario (origianlly Figure 7b, now Figure 8b)</li> </ul> </li> <li>images_and_vidoes_for_paper.zip <ul> <li>has all the images, videos, and some figures from the main body of the paper and the supplmental material. Updated in this version.</li> </ul> </li> <li>Invasive_cellular_front.zip <ul> <li>Has results for each ECM scenario: random, parallel, and perpindicular orientations and mixed ECM conditions. New to this data repository.</li> </ul> </li> <li>python_imaging.zip <ul> <li>Base modules and examples for producing images (tested on Python 3.9). Updated in in this verison</li> </ul> </li> <li>SM_Fig_4b_leader_follower_decreased_remodeling.zip</li> <li>stochastic_replicates.zip <ul> <li>Contains stochastic replicates for the collective migration, fibrosis, and invasive carcinoma models and source code for all.</li> </ul> </li> <li>stochastic_replicates_invasive_cellular_front.zip <ul> <li>Contains stochastic replicates for the invasive cellular front scenarios. New to this data repository.</li> </ul> </li> </ul>
Data for: SUN2 regulates mitotic progression in response to extracellular matrix rigidity
<p>How cells adjust their growth to the spatial and mechanical constraints of their surrounding environment is central to many aspects of biology. Here we examined how ECM rigidity affects cell division. We found that cells divide more rapidly when cultured on rigid substrate. While we observed no effect of ECM rigidity on rounding or post-mitotic spreading duration, we found that changes in matrix stiffness impact mitosis progression. We noticed that ECM elasticity up-regulates the expression of the LINC complex component SUN2, which in turn promotes metaphase-to-anaphase transition by acting on mitotic spindle formation. Whereas when cells adhere on soft ECM, low levels of SUN2 expression perturb astral microtubule organization and delay the onset of anaphase.</p>
Single-cell and spatial transcriptomics of cardiac neural crest reveal a dual role of vinculin in Tgf beta signaling and cell-extracellular matrix interaction during cardiac outflow tract development
<p>single-cell RNA-seq data analysis:</p> <p>all.cncc.combined.EMBO.mapped.Rdata: public CNCC single-cell RNA-seq data integration</p> <p>E13.5_CNCC_merged_updated.Rdata: single-cell RNA-seq data of E13.5 CNCC generated in Elly lab</p> <p>all.seurat.GFP.Rdata: scRNA-seq data with GFP detected</p> <p>visium.merge_AB.control.Rdata: R processed ST data for slice A and B</p> <p>visium.merge_CD.mutant.Rdata: R processed ST data for slice A and B</p> <p> </p>
Role of Extracellular Matrix in the Development of Airway Remodeling in Asthma
ClinicalTrials.gov study NCT03388359. IPD Sharing: NO. Countries: 1. Publications: 10.
Randomized Study of Coronary Revascularization Surgery With Injection of WJ-MSCs and Placement of an Epicardial Extracellular Matrix
ClinicalTrials.gov study NCT04011059. IPD Sharing: NO. Countries: 1. Publications: 32.
In-Vivo Assessment of Adipose Allograft Extracellular Matrix in Abdominoplasty Patients
ClinicalTrials.gov study NCT02845180. IPD Sharing: UNDECIDED. Countries: 1. Publications: 4.
Data for: SUN2 regulates mitotic progression in response to extracellular matrix rigidity
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Synaptic connectivity and neuronal network activity changes after extracellular matrix depletion
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.